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Forum: De novo discovery 06-30-2014, 06:31 PM
Replies: 15
Views: 2,297
Posted By pmart1
I was able to run it and these were the resulting...

I was able to run it and these were the resulting metrics.

scaffoldMetrics
numberOfScaffolds = 51;
numberOfBases = 145548;
avgScaffoldSize = 2853;
N50ScaffoldSize =...
Forum: De novo discovery 06-30-2014, 02:35 PM
Replies: 15
Views: 2,297
Posted By pmart1
I do have Newbler on my other computer. When I...

I do have Newbler on my other computer. When I get home, I will run it and post the results. Thank you very much for all of your help! It is very appreciated.
Forum: De novo discovery 06-30-2014, 02:09 PM
Replies: 15
Views: 2,297
Posted By pmart1
Magic Number: 0x2E736666 Version: 0001 Index...

Magic Number: 0x2E736666
Version: 0001
Index Offset: 551942992
Index Length: 4131866
# of Reads: 206557
Header Length: 840
Key Length: 4
# of Flows: 800
Flowgram Code: 1
Flow Chars:...
Forum: De novo discovery 06-30-2014, 01:55 PM
Replies: 15
Views: 2,297
Posted By pmart1
(Strain name).sff. I'm not sure how to open it.

(Strain name).sff. I'm not sure how to open it.
Forum: De novo discovery 06-30-2014, 01:51 PM
Replies: 15
Views: 2,297
Posted By pmart1
The libraries are from an old strain that...

The libraries are from an old strain that perished in a power outage so we cannot run any further sequencing.
Forum: De novo discovery 06-30-2014, 01:35 PM
Replies: 15
Views: 2,297
Posted By pmart1
Pardon me, the 454 is 500bp double ended. I'm...

Pardon me, the 454 is 500bp double ended. I'm actually an intern in a lab and all of this (including linux) is extremely new to me.
Forum: De novo discovery 06-30-2014, 12:14 PM
Replies: 15
Views: 2,297
Posted By pmart1
Thank you for the suggestion, Martin! I will have...

Thank you for the suggestion, Martin! I will have to try that. I've never used MIRA before. Also, would you be able to share your code for the 454 trimming?
Forum: De novo discovery 06-30-2014, 11:34 AM
Replies: 15
Views: 2,297
Posted By pmart1
Smile illumina 454 de novo hybrid

Hi all,

I am currently trying to assemble a 5mb bacterial genome. I have 43bp single end reads from an Illumina Genome Analyzer IIx and 500bp double end reads from a Roche 454 GS FLX and was...
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